Hi priya http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx these link may be help to you
i like to know how to calculate index groups for my micelles.. since i am having two micelles , one having 8molecules and another having 2molecules.. residue number for that 2molecule micelle is 2 and 7.. can you help me how to form index group for this two micelles.. make_ndx command need to be used . i searched but couldnt get the point clearly .. make_ndx –f .....gro/pdb –o my_index.ndx You will see the following output (we left out the descriptive info at the beginning) followed by acommand prompt (>). Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 129 Protein residues There are: 10824 Water residues There are: 8 Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 34440 atoms 1 Protein : 1960 atoms 2 Protein-H : 1001 atoms 3 C-alpha : 129 atoms 4 Backbone : 387 atoms 5 MainChain : 517 atoms 6 MainChain+Cb : 634 atoms 7 MainChain+H : 646 atoms 8 SideChain : 1314 atoms 9 SideChain-H : 484 atoms 10 Prot-Masses : 1960 atoms 11 non-Protein : 32480 atoms 12 Water : 32472 atoms 13 SOL : 32472 atoms 14 non-Water : 1968 atoms 15 Ion : 8 atoms 16 CL : 8 atoms 17 Water_and_ions : 32480 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom & 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index > Use the ‘r’ command to enter the list of residue numbers that represent the N & C termini of the triple helix. > r 1 36 37 72 73 108 15 r_1_36_37_72_73_108 : 51 atoms Note: You may also use a dash to specify a residue number range (e.g. to specify residues 1 to 36 use > r 1-36) ... OR, better yet, lets specify a residue range only including backbone atoms. Do this with the ampersand for example ... > r 1-36 & a C N CA The default name (r_1_36_37_72_73_108 ) giving to the new index group that you have just created is cumbersome. Lets rename it using the name command. We will use the index group # (15) in the command. > name 15 Terminal > v(Verbose) >h for help give information on index tool >q for quite.. And use these index file by specifying it for further analysis... you can make group by specifying atom no 0r range of atom that form micelle .. Have a nice day........ With Best Wishes,
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
